We assessed whether cardiac MRI (CMR) and echocardiography (echo) have significant differences measuring left ventricular (LV) wall thickness (WT) in hypertrophic cardiomyopathy (HCM) as performed in the clinical routine. Retrospectively identified, clinically diagnosed HCM patients with interventricular-septal (IVS) pattern hypertrophy who underwent CMR and echo within the same day were included. Left Ventricular WT was measured by CMR in two planes and compared to both echo and contrast echo (cecho). 72 subjects, mean age 50.7 ± 16.2 years, 68 % males. Interventricular septal WT by echo and CMR planes showed good to excellent correlation. However, measurements of the postero-lateral wall showed poor correlation. Bland-Altman plots showed greater maximal IVS WT by echo compared to CMR measurement [SAX = 1.7 mm (-5.8, 9.3); LVOT = 1.1 mm (-5.6, 7.8)]. Differences were smaller between cecho and CMR [SAX = 0.8 mm (-9.2, 10.8); LVOT = -0.2 mm (-10.0, 9.6)]. Severity of WT by quartiles showed greater differences between echo and SAX CMR WT compared to cecho. Echocardiography typically measures greater WT than CMR, with the largest differences in moderate to severe hypertrophy. Contrast echocardiography more closely approximates CMR measurements of WT. These findings have potential clinical implications for risk stratification of subjects with HCM.